PE-MMR can be used to create a MGF file with refined parent ion masses and charges, which can lead to more accurate search results from MS/MS spectra.
The Concatenated Text File Splitter can be used to split apart the concatenated file to re-create the individual text files (creating one file per spectrum).
MZRefinery is a software tool for correcting systematic mass error biases in mass spectrometry data files.
The Flexible File Sort Utility is a command line application that sorts a text file alphabetically (forward or reverse).It supports both in-memory sorts for smaller files and use of temporary swap files for large files.
Console application that reads a protein FASTA file and splits it apart into a number of sections. Although the splitting is random, each section will have a nearly identical number of residues.
DataProcessing toolbox for running MSGF+ and MASIC, then merging the results. Uses Windows batch files to automate the process for a folder of Thermo .Raw files
Windows graphical user interface tool for viewing LC-MS data and identifications.
InfernoRDN can perform various downstream data analysis, data reduction, and data comparison tasks including normalization, hypothesis testing, clustering, and heatmap generation.
MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
DeconMSn creates spectrum files for tandem mass spectrometry data.